[English] 日本語
Yorodumi
- PDB-1n10: Crystal Structure of Phl p 1, a Major Timothy Grass Pollen Allergen -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n10
TitleCrystal Structure of Phl p 1, a Major Timothy Grass Pollen Allergen
ComponentsPollen allergen Phl p 1
KeywordsALLERGEN / Plant allergen / phl p 1 / expansin / immunoglobulin-like fold / double-psi beta barrel / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


sexual reproduction / extracellular region
Similarity search - Function
Major pollen allergen Lol pI / Expansin/Lol pI / Rare lipoprotein A (RlpA)-like double-psi beta-barrel / Expansin, Cellulose-binding-like domain profile. / Expansin, cellulose-binding-like domain / Expansin C-terminal domain / Expansin/pollen allergen, DPBB domain / Expansin, family-45 endoglucanase-like domain profile. / Expansin, cellulose-binding-like domain / RlpA-like protein, double-psi beta-barrel domain ...Major pollen allergen Lol pI / Expansin/Lol pI / Rare lipoprotein A (RlpA)-like double-psi beta-barrel / Expansin, Cellulose-binding-like domain profile. / Expansin, cellulose-binding-like domain / Expansin C-terminal domain / Expansin/pollen allergen, DPBB domain / Expansin, family-45 endoglucanase-like domain profile. / Expansin, cellulose-binding-like domain / RlpA-like protein, double-psi beta-barrel domain / Expansin, cellulose-binding-like domain superfamily / Lytic transglycolase / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pollen allergen Phl p 1
Similarity search - Component
Biological speciesPhleum pratense (timothy grass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsFedorov, A.A. / Ball, T. / Leistler, B. / Valenta, R. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
Citation
Journal: To be Published
Title: X-ray Crystal Structure of Phl p 1, a Major Timothy Grass Pollen Allergen
Authors: Fedorov, A.A. / Ball, T. / Leistler, B. / Valenta, R. / Almo, S.C.
#1: Journal: INT.ARCH.ALLERGY.IMMUNOL / Year: 1997
Title: X-ray Crystal Structures of Birch Pollen Profilin and Phl p 2
Authors: Fedorov, A.A. / Ball, T. / Valenta, R. / Almo, S.C.
#2: Journal: STRUCTURE / Year: 1997
Title: The molecular basis for allergen cross-reactivity: crystal structure and IgE-epitope mapping of birch pollen profilin
Authors: Fedorov, A.A. / Ball, T. / Mahoney, N.M. / Valenta, R. / Almo, S.C.
History
DepositionOct 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 3, 2021Group: Structure summary / Category: audit_author / chem_comp
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pollen allergen Phl p 1
B: Pollen allergen Phl p 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9744
Polymers52,5312
Non-polymers4422
Water0
1
A: Pollen allergen Phl p 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4872
Polymers26,2661
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pollen allergen Phl p 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4872
Polymers26,2661
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.685, 65.526, 144.769
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

-
Components

#1: Protein Pollen allergen Phl p 1 / Phl p I


Mass: 26265.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phleum pratense (timothy grass) / Gene: PHLPI / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43213
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.584 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, ammonium sulfate, tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 1.01 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 29, 2002
RadiationMonochromator: Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 12934 / Num. obs: 12934 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 39.6
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 8.2 / % possible all: 84.3

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.9→20 Å / Rfactor Rfree error: 0.01 / Cross valid method: througout / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 664 5.1 %RANDOM
Rwork0.239 ---
all0.243 12934 --
obs0.243 12934 98.6 %-
Solvent computationSolvent model: flat model / Bsol: 10.04 Å2 / ksol: 0.271776 e/Å3
Displacement parametersBiso mean: 45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3512 0 28 0 3540
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.55
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it2.571.5
X-RAY DIFFRACTIONc_mcangle_it4.332
X-RAY DIFFRACTIONc_scbond_it3.962
X-RAY DIFFRACTIONc_scangle_it6.512.5
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 61 5.1 %
Rwork0.298 1932 -
obs-1213 95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide.param

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more